Recommended problems from chapter 18: 3,5,7,8,9,10,11,12,13,14,16,17,21,22 Glycolysis is the sequence of reactions that are used to break down glucose. Glycolytic reactions are conserved through most organisms, so the sequence of reactions (including substrates, products, and enzymes) is almost the same in all organisms. Clearly, this is a successful approach to sugar catabolism. Glycolysis overview Steps 1 and 3 involve energy investment in the form of ATP hydrolysis. Step 6 generates 2 NADH molecules Steps 7 and 10 together generate 4 ATP molecules. 1 Reaction 1. Hexokinase ATP + Glucose → Glucose-6-phosphate + ADP + H+ This step depends on hexokinase and magnesium. A kinase is an enzyme that transfers a phosphoryl group to a substrate. Hexokinase can transfer a phosphoryl group to many 6-carbon sugars, such as D-mannose and D-fructose. Glucokinase catalyzes the same reaction in the liver, and this enzyme is primary involved in maintaining blood sugar levels. The first step - hexokinase ATP + Glucose → Glucose-6-phosphate + ADP + H+ Magnesium ions are required for hexokinase activity. Magnesium “shields” or “engages” the negative charges of the oxygen atoms and makes the γ-phosphorus more susceptible to nucleophilic attack by the C6 hydroxyl oxygen. Uncomplexed ATP is an inhibitor of hexokinase activity. Would you expect uncomplexed ATP to be a competitive or a non-competitive inhibitor of hexokinase? 2 Water is excluded from the active site of hexokinase in the presence of glucose Uncomplexed enzyme + glucose complexed enzyme:glucose Why is it favorable to exclude water from the active site during phosphoryl transfer? Reaction 2. Phosphoglucose isomerase Both G6P and F6P exist predominantly in a closed ring structure, so the reaction requires ring opening, isomerization, then ring closure. 3 Proposed mechanism of phosphoglucose isomerase Reaction 3 - phosphofructokinase The uncoupled reaction is given by: Fructose-6-P + Pi → Fructose-1,6-bisphosphate ∆G°’ = +16.3 kJ/mol If ATP hydrolysis is coupled to the reaction, the reaction becomes Fructose-6-P + ATP → Fructose-1,6-bisphosphate + ADP ∆G°’ = -14.2 kJ/mol This reaction “commits” the reaction to go to the right under standard conditions. 4 Reaction 3. Regulation of PFK by ATP Is ATP an inhibitor or activator of PFK? Does this make sense in terms of the final outcome of the pathway? Reaction 3. Regulation of PFK by AMP AMP is a positive allosteric effector (an activator) of PFK. The cellular concentrations of AMP, ADP and ATP are regulated by the enzyme adenylate kinase: ADP + ADP ↔ AMP + ATP Keq = 0.44 Typical ADP levels are 9% of ATP, and AMP levels are less than 1% of ATP. Because of this equilibrium, the concentration of AMP can rise very fast as a result of ATP hydrolysis. For example, by how much will the concentration of AMP rise if the concentration of ATP falls by 10% as a consequence of hydrolysis into ADP + Pi? Assume that the typical concentration of ATP is 1.5 mM. This is an example of an exceptionally elegant feedback regulatory circuitry. As [ATP] is decreased, [AMP] is increased rapidly due to the equilibrium above. This information is “read” by the glycolytic pathway as a signal to increase production of ATP. 5 Reaction 3. Regulation of PFK by citrate Citric acid is a negative allosteric effector of PFK. This achieves a coupling of the citric acid cycle and glycolysis. Glycolysis “feeds” the citric acid cycle by the production of pyruvate and acetyl CoA. Because the main function of the citric acid cycle is the production of ATP, when this pathway is saturated glycolysis is slowed such that glucose is not committed into glycolysis as fast. Reaction 4. Aldolase Cleavage of F-1,6-BP into DHAP and GAP. Note the carbonyl at C2. 6 Uncatalyzed aldol cleavage The enolate transition state is stabilized by the multiple electron resonances. This is due to the ability of the carbonyl oxygen to withdraw electrons. The carbonyl at C2 of FBP is a consequences of reaction 2, the isomerization of G6P to F6P. This is beneficial because the aldolase reaction with F6P yields two transition state compounds that can be interconverted and thereby stabilize the transition state. What catalytic strategy(ies) would you expect to be used by an enzyme to facilitate the rate of this reaction? Reaction 4. Mechanism of class I aldolase - animal and plant cells 1. Substrate binding. 7 Mechanism of class I aldolase - animal and plant cells 2. Chain opening and schiff-base formation between the enzyme lysine and the open chain. •The enzyme + substrate complex is inactivated by the presence of NaBH4 due to the transfer of a hydride ion to the imine carbon. The resulting ES complex is stable and does not go through subsequent steps (what type of inhibitor is NaBH4?). •Incubation of a 14C-labeled substrate with the enzyme + NaBH4 followed by complete digestion of the enzyme to yield individual amino acids can be used to identify a modified lysine residue. •Incubation of the enzyme alone with NaBH4 followed by removal of NaBH4 results in no inhibition. 3. Enamine intermediate formation within class I aldolase Step 3 of this reaction results in aldol cleavage, release of GAP, and Enamine-enzyme covalent complex formation. The iminium ion is a better electron withdrawing group than the carbonyl oxygen of the precursor. The enamine intermediate is more stable than the enolate intermediate of the uncatalyzed reaction, and this results in a substantial rate enhancement in the enzyme-catalyzed reaction. 8 4. Protonation of the enamine intermediate within class I aldolase results in iminium ion (protonated Schiff base) formation 5. Hydrolysis of the iminium ion and release of DHAP 9 Class II aldolases in fungi, algae, and bacteria The enolate intermediate is stabilized by a zinc or iron(II) ion within the enzyme. GAP (an aldose) DHAP (a ketose) Reaction 5. Triose phosphate H isomerase (TIM) H O C H C OH The two 3-carbon products of enolase are H C OH C O interconverted by TIM. - - The enediol intermediate pathway is CH2OPO3 CH2OPO3 supported by the binding of the transition state analogs phosphoglyco- hydroxamate and 2-phosphoglycolate to the enzyme. The transition state analogs bind the H OH enzyme with 100 to 155 fold increased C affinity, in comparison to the an enediol intermediate physiological substrates. This allows a C OH quantitative assessment of the transition CH OPO - state stabilization achieved by the 2 3 enzyme. OH - N - O O O C C - - CH2OPO3 CH2OPO3 Phosphoglyco- 2-Phosphoglycolate hydroxamate 10 Summary of the first stage of glycolysis The second stage of glycolysis - generation of additional high energy compounds Reaction 6. Oxidation and phosphorylation of GAP By glyceraldehyde-3- phosphate dehydrogenase. The favorable aldehyde oxidation reaction contributes free energy in order to drive the generation of the high-energy acyl phosphate and reduction of NAD+ into NADH. Overall, however, the reaction is slightly unfavorable under standard conditions. 11 Mechanistic studies of GAPDH 1. GAPDH is inhibited by alkylation with stoichiometric amounts of iodoacetate, and a carboxymethylcysteine is present among the hydrolysis products of the modified enzyme. The enzyme must contain an essential cysteine residue. 2. GAPDH transfers 3H from the C1 of GAP to NAD+. Mechanistic studies of GAPDH 32 3. GAPDH can exchange P from Pi in solution to the product analog acetyl phosphate. What substrate binding mechanism is supported by these results? 12 Catalytic mechanism of GAPDH, proposed by D. Trentham 1. Substrate binding. Catalytic mechanism of GAPDH, proposed by D. Trentham 2. The essential sulfhydryl group acts as a nucleophile, attacks the aldehyde, and a thiohemiacetal is formed. 13 Catalytic mechanism of GAPDH, proposed by D. Trentham 3. An acyl thioester is formed by oxidation of the thiohemiacetal. H+ is directly transferred to NAD+. This is a covalent high-energy intermediate that has been isolated. Catalytic mechanism of GAPDH, proposed by D. Trentham 4. NADH dissociates and NAD+ binds. 5. 1,3-bisphosphoglycerate (1,3-BPG) is formed by the nucleophilic attack of Pi.on the carbonyl carbon. 14 Reaction 7, phosphoglycerate kinase - the first ATP generation reaction Phosphoglycerate kinase - the first ATP generation reaction As in hexokinase, the 2 lobes of the enzyme close up upon substrate binding. This excludes water from the active site (why is this desirable for a phosphoryl transfer reaction?). 15 Coupling the GAPDH and PGK reactions + Reaction 6. GAP + Pi + NAD ↔ 1,3-BPG + NADH ∆G°’ = +6.7 kJ/mol Reaction 7. 1,3-BPG + ADP ↔ 3PG + ATP ∆G°’ = -18.8 kJ/mol Here the favorable PGK reaction seems like it “pulls” the slightly unfavorable GAPDH reaction. In the cell, ∆G for both reactions is approximately 0. Reaction 8. Phosphoglycerate mutase Although on the surface this might look like a facile reaction, it is actually quite involved. 16 Proposed catalytic mechanism of phosphoglycerate mutase A key aspect of this mechanism is the presence of a phospho-histidine modified residue that is essential for catalysis. Proposed catalytic mechanism of phosphoglycerate mutase If 2,3-BPG dissociated from the enzyme, would this enzyme now become inactive? How can this condition be reversed? 17 Reaction 9. Enolase-dependent generation of the second “high energy” product This enzyme is divalent cation-dependent. Mg2+ is used most often, but other divalent cations will do as well. F- ions inhibit enolase by binding to magnesium. NaF inhibits glycolysis, and is therefore a potent poison. Reaction 10. Generation of the second ATP and pyruvate by pyruvate kinase 1. Nucleophilic attack by the ADP β-phosphoryl oxygen on the PEP phosphorus generates ATP and enolpyruvate. ∆G°’ = -16 kJ/mol 2. Tautomerization of enol pyruvate to pyruvate.